Actual pharmaceutical wastewater was pretreated with ozone microbubbles and compared with the treatment processes of nitrogen microbubbles, ozone common bubbles, and nitrogen common bubbles. The removal process and performance of suspended solids (SS) and organic compounds were investigated. The results showed that ozone microbubble treatment with strong adsorption-flotation-oxidation effects could enhance SS removal significantly, and the corresponding SS removal efficiency reached 81.67% at 60 min. The SS particle size was reduced, and the negative charge on the SS surface was simultaneously changed into a positive charge. Microbubble ozonation with a strong·OH oxidation effect also significantly enhanced the degradation and removal of organic compounds. The removal efficiency of soluble COD (SCOD) reached 36.60% at 60 min, and the SCOD removal was accelerated after the SS removal. The removal efficiency of UV254 also reached 36.91%. The biodegradability was improved, and the biological toxicity was obviously eliminated. The analysis of three-dimensional fluorescence and GC-MS showed that the macromolecular organic compounds with complex structure could be oxidized and decomposed efficiently with microbubble ozonation, resulting in the aromatic reduction in organic compounds in wastewater. Therefore, microbubble ozonation could be considered as an efficient and feasible pretreatment method for high concentration and refractory pharmaceutical wastewater.